Monday, February 15, 2010

Reflection

While having reflecting on three major topics studied during the semester in biochemistry and how they connect with the classroom discussion, I prepare to enter my semester end blog.
The question: How would you connect with the topics today, i.e. what did you know before the course? What have you learned about these three topics during the course?
The topics:
The steroid group
Sex hormones
The sodium/potassium pump
While discussing these three topics of interest, I will be leaning heavily upon the class text Biochemistry, by Campbell, Farrell & Shawn and PowerPoint class notes.
My knowledge for all three topics discussed below was on a very basic level. The knowledge of both structure and function was above my level of knowledge at the start of class in late January.
The first topic that I wish to discuss is the steroid group cholesterol, perhaps the most common, but least recognized as a steroid. Cholesterol is a critical steroid when it comes to the proper function of the human body. The primary structure is uniform, comprised of three (6) membered rings and a single (5) membered ring, followed by a carbon chain of varying lengths. Cholesterol serves as an important steroid, critical to the structural integrity of our cells. Cholesterols also serve as precursors to many other important biomolecules. Embedded in the Phospolipid bilayer, cholesterol add to the cell membranes rigidity and help to form bonds that firm up these basic but important cell wall structures and ultimately serve to give the body strength through a well-connected muscular undercarriage. Finally, it is important to mention that there are two forms of cholesterol HDL and LDL. HDL is high density, the “good” and LDL is low density or the “Bad” form.
Google to Blog Spot for a page on Cell wall: apbio82007.blogspot.com/.../cell-membrane.html
The sex hormones are arguably the next most common steroid group besides cholesterol, due to the important effects that they mediate and the fact that they are cholesterol derivatives and without regular intake of cholesterol from our diet, our bodies would have to expend drastic amounts of energy modifying other precursor molecules into essential hormones. They include, but are not limited to testosterone, estrogen and progesterone. These steroids are critical to normal function of primary sexual function as well as other various types of processes. These steroids follow the ring structure model listed above for cholesterol, the 6:6:6:5 ring fusion conformation, giving them steroid status, but have undergone various chain modifications to make them into specific sex hormones.
The second area of interest is the biomolecule the triacylglycerol group. These molecules are composed of three fatty acids and one glycerol molecule joined by three separate dehydration reactions, which forms an ester linkages between the fatty acids and the glycerol. These molecules are found in adipose tissue and carry a 2:1 ration for energy, when comparing a molecule of triacylglycerol to a carbohydrate or protein. These molecules are truly the fuel of humanity.

The third and final topic of reflection is the Potassium/Sodium pump. Specifically, the action of the three sodium molecules brought out of the typical human cell, the two Potassium molecules brought into the typical human cell, and the action potential given by one ATP or specifically one Phosphate atom’s bond energy to drive the reaction. Note: if the process is reversed, in response to a change in the direction of the gradient, although more rare, ATP is produced as a result. This is an example of a membrane protein within a cell changing conformation, in a number of different ways, at a number of different sites, to result in the correct substrates attaching to the correct areas and the complicated function of ion transport.
My take-away point for this semester is the newfound understanding of complexity when it comes to biomolecules and their roles in the workings of the human body. It may appear simple when looking at just one topic on its own, but as I have learned this semester, the synthesis of any number of systems with one another, describes a system of almost infinite complexity.

In all three cases, I have possessed a reasonably functional knowledge of the subject matter. The advantage of taking Biochemistry has been to tie in the working knowledge between these separate topics and thus advancing ones knowledge of the topics individually and collectively.
Thanks, Biochem you’re the best.
MCB

Energy Metabolism

How would you explain to a friend, energy metabolism, (i.e. glucose entering the body and energy creation} using your knowledge from Biochemistry?

Well I am not so sure that my friends would appreciate having me tell them about energy intake and metabolism, but here it goes.

We take in complex forms of food in order to survive. It is the bodies job to break them down and metabolize the less complex more fully catabolized products to make and store energy from intermediates. The sugar glucose and its stored form glycogen are the primary intermediates used in energy metabolism in the human body. Without glucose we last about 4 minutes before our bodies start to shut down. Within a half hour, our bodily extreme short-term stores would be tapped and we would be dead. The key word is stores. The body stores energy for normal fasting and times of famine in the form of fat and muscle in the case of extreme famine. It would be likely that we would just run out of glucose like we might run out of air when we stop breathing, but extreme athletes must not only keep up their critical electrolyte balance, but also their blood glucose levels. Diabetics deal with swings in glucose levels on a daily basis, due to the lack of regular or functional insulin production. This condition can absolutely be fatal when the sugar unbalance swings to far in either direction. The body has evolved under the condition known as homeostasis, meaning that the body self regulates to stay in working balance. The sugar balance regulation in our blood is no exception.

In addition to the glucose in blood, glucose leaving the blood and entering each cell in our bodies is as, if not more important than any other form. The cells in the body utilize the symbiont organelle the mitochondria to produce our energy currency AMP, ADP, and ATP. These molecules are our source of life. The energy stored in advance in the bonds of these and a select group of other molecules power all of the chemical reactions in our bodies, every second of the day.

Well this was the basic knowledge that I have learned about glucose metabolism and the subsequent ATP production once glucose has entered our bodies.

MCB

Again, Knowledge

What knowledge have you connected with past knowledge during Biochemistry?

Using the text, Campbell & Farrell, Biochemistry and classroom PowerPoint presentations, I wish to confer my new and improved understanding of enzymes and their specific characteristics. First and most importantly, is the fact that their are two main groups of enzymes, differentiated by the form of activation. The naming of both groups follows a the same pattern. That is the descriptive of what it pertains or acts on and the suffix "-ase". Lipase is active on lipids and is a typical naming example.

The first and probably the more simple of the two is the non-allosteric enzyme. This form of enzyme is either activated or inhibited by a non-competitive inhibitor through the active site or main physical shape specific connection to other molecules; most often taking the shape of proteins. This category of enzymes follow a very specific and well defined mathematical model called the Michaelis Menton model, the equations and specifics of which are readily available on line. This model when graphed produces a hyperbolic curve, making it easy to pick out when all that you have to go by is a graph on a exam or lab practical.

The second and probably more complex of the two is the allosteric enzyme. The allosteric enzyme is so named, for its additional "allosteric" activation site. Instead of following the Michaelis Menton model for behavior, the allosteric enzyme group instead follows the "sequential model". Hemoglobin is a terrific and familiar example of this model, exhibiting this type of binding type of binding. In the case of Oxygen binding on the individual heme subunits, the binding affinity increases with 1 to 4 Oxygen atoms bound. This transforms the enzyme from a type T to a Type T-R, to a Type R as the atomic unit substrates bind to the quaternary subunits.

Finally and possibly more important is the action of the enzymes no matter the type. Enzymes are catalysts first and foremost. All catalysts, however, are not created equal. The enzymatic catalytic reactions are several orders of magnitude better than the best non-enzymatic catalyst reaction. This means that the reaction in living organisms can be fast enough and efficient enough to maintain the various complex systems of life. In short, we owe much of who and what we are to enzymes.

MCB

Biochemistry Web Site

Find an interesting Biochemistry web site. Describe and place link to site in blog.

Site: http://www.medicalnewstoday.com/sections/biology-biochemistry/

The above website is a great resource for not only doing research, but also just reading about: Medical topics, Prosthetic Device topics, Biochemical topic, biology topics and much more. The site is almost as diverse as biochemistry itself. I enjoy the variety of articles listed. Whether you are from a medical, research, industrial high-tech or other background, there is something for just about everyone.
The following are the new topics/full articles from today, March 8th, 2010 as listed on the site:

* Ritalin Boosts Learning By Increasing Brain Plasticity
* In Stanford, Mathematical Innovation Turns Blood Draw Into Information Gold Mine
* New Sensor Array Detects Single Molecules For The First Time
* Experimental Vaccine Protects Monkeys Against Chikungunya
* Evolutionary Biologist: Studies The Co-Evolution Of Humans And Diseases

Diverse as biochemistry itself right? Well maybe not, but there is potentially something for everyone. The health video section is a powerful learning tool for those in the medical profession, the public and of course students. Possibly best of all is that the site is free to the public and constantly changing and updating from day to day.

MCB

Knowledge

* What knowledge have you made connections with during this semester of Biochemistry?

It is as of yet, early in the semester, but we have already covered so much material. One of the topics that I have personally found most interesting is "RNA-World Theory". The source for this theory are the class notes and the class text. (Campell & Farrell, 2010). This theory looks at the origin of the world in light of the big bang theory and early earth chemistry shown in the fossil geological record.

The premise of the theory is that the basic atomic atoms started to form and then degraded into the elements over time. This scenario gives the earth the building blocks that it would need for life, especially H2O. When looking at a pool of resources, one must speculate that a series of basic elements must be able to be induced, by available means such as solar winds, electrical charges, etc. to form more complex molecules. The first and most important chemicals were theorized to be phospho-lipids, which could and do make enclosed spherical membranes when exposed to water. It is in this small enclosed vesicle that the first self replicating molecules that could perform limited catalyzation must have arose, or so the theory goes.(Calvalier-Smith, Origin of Mitochondria, 2006) DNA was one molecule that was theorized to have been this potential unit of life. Protein was another. DNA turns out to only have coding abilities and protein turns out to have only catalytic abilities. RNA, however, has been found in laboratory test to have both. RNA could have encoded and catalyzed its own replication. This way of looking at the early earth is a powerful view of how life could have come from seemingly nothing.(Futuyma, 2010, Evolution Text) According to Futuyma, 2010, once you have a coded replicateable molecule, natural selection could take hold over a vast number of years. Say a couple of billion years for starter and then "wham" you have basic life, or something close to that account.(Calvalier-Smith, Origin of Mitochondria, 2006)

When this type of basic first step theory is laid out in a realistic stepwise manor and it is tempered with enough time, it can make for a good argument. No one alive today was present at the beginning of the earth's history, this we know with absolute certainty, except possibly god; that begs the question "where were god's beginnings and who or what was present for that moment and how could all of this something come from nothing". The point is that we can never know with absolute certainty what happened billions of years ago, but it is the job of science to ask appropriate questions about the origins, no matter how uncomfortable that makes "some" people. I happen to list myself as one of the "people" who was uncomfortable with this type of questioning. I will say that the benefit of a biological education is the slow stepwise process that helps to bring ones understanding of these complex topics, such as evolution, into focus very slowly and most importantly without the non-science noise that is present in real world debates/arguments on these subjects. We are not in theology school, we did not sigh up for theology school and it is not our job to act as if we had. In closing, I see more clearly that it is not the job of science to make contact with god, nor prove an omnipotent creators case for existence. This task of proving this case would be for an omnipotent creator and/or the various theologians of the world, not your average nor extraordinary, for that matter, scientist to make. I do not wish to sound sarcastic, being of "faith" myself, it is just that I feel that I understand the role of science more clearly today and no longer with for science to apologize for doing what its most basic charters would mandate it to do. (Personal opinion)

MCB